It's done all the time, the software I use doesn't give a warning. Contact the support people for your PCB software, they should tell you how to avoid the problem. Or, just ignore the warnings, the boards should come out OK. You could check the Gerbers with a program like GC-Prevue to make sure.
They look like the footprint for an alternative package, probably the TQFP-44 variant. Having both footprints: QFN (the leadless package that is installed) and the alternative TQFP variant allows a single board to be used depending on the availability of either part for more flexible BOM management. You could also use it for testing, as originally suggested as well.
Best Answer
They are there to allow for wave soldering. As the solder flows on the legs, any excess can end up on those pads, not shorting out the pins of the IC.